Thanks for the quick response!
I have a feeling this is something silly that I'm missing. As a reality
check I simply created a copy of the biomart.xml tool.xml file and called
it test_me.xml. I changed the tool_id and GALAXY_URL in the xml file as
you'll see and added a link in my tool_config. Selecting this tool from
the Get Data folder brings me to Biomart as expected. When I hit "go", I
have the same issue of just being redirected to the welcome page. The
server output is shown below. The unchanged biomart tool continues to work
Galaxy server output:
127.0.0.1 - - [01/Dec/2011:08:08:27 -0700] "POST
302 - "
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:8.0.1) Gecko/20100101
Here's my Galaxy revision info:
user: Nate Coraor <n...@bx.psu.edu>
date: Thu Sep 29 16:45:19 2011 -0400
P.S. It's my pleasure to use Galaxy! ;)
On Thu, Dec 1, 2011 at 7:06 AM, Daniel Blankenberg <d...@bx.psu.edu> wrote:
> Hi James,
> Can you let us know which revision of Galaxy that you are using (hg head)
> and any log output that appears when accessing or running the tool? Also
> the list of parameters and values that are being POSTed to Galaxy and a
> copy of your tool.xml file would be useful.
> Thanks for using Galaxy,
> On Dec 1, 2011, at 5:08 AM, James Ireland wrote:
> I've been attempting to return data to Galaxy via the synchronous data
> depositing protocol. Using the Biomart, UCSC Table Browser, etc as
> examples in the data_source tools directory, I've been able to get the
> initial GET request to my site just fine. However, when I POST back to
> galaxy I immediately get a redirect to the welcome page and Galaxy never
> resubmits back to my site.
> I was wondering if there is more to the protocol than is covered here:
> http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources or perhaps
> configuration I need to perform on my local Galaxy installation to
> correctly handle the POSTs back to tool_runner? Also, are there any code
> examples I should be looking at?
> Thanks for your help!
> J Ireland
> www.5amsolutions.com | Software for Life(TM)
> m: 415 484-DATA (3282)
> Please keep all replies on the list by using "reply all"
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www.5amsolutions.com | Software for Life(TM)
m: 415 484-DATA (3282)
If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
TODO: Hack to get biomart to work - the 'add_to_URL' param can be eliminated when the Biomart team encodes URL prior to sending, meanwhile
everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed at their end.
<tool name="BioMart" id="test_me" tool_type="data_source" version="1.0.1">
<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
<inputs action="http://www.biomart.org/biomart/martview" check_values="false" method="get" target="_top">
<display>go to BioMart Central $GALAXY_URL</display>
<param name="GALAXY_URL" type="baseurl" value="/tool_runner/test_me" />
<request_param galaxy_name="URL" remote_name="URL" missing="">
<append_param separator="&" first_separator="?" join="=">
<value name="_export" missing="1" />
<value name="GALAXY_URL" missing="0" />
<request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" >
<value galaxy_value="tabular" remote_value="TSV" />
<request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
<request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" />
<request_param galaxy_name="organism" remote_name="organism" missing="" />
<request_param galaxy_name="table" remote_name="table" missing="" />
<request_param galaxy_name="description" remote_name="description" missing="" />
<request_param galaxy_name="name" remote_name="name" missing="Biomart query" />
<request_param galaxy_name="info" remote_name="info" missing="" />
<data name="output" format="tabular" />
<options sanitize="False" refresh="True"/>
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